Safety in multi-assembly via paths appearing in all path covers of a DAG
A multi-assembly problem asks to reconstruct multiple genomic sequences from mixed
reads sequenced from all of them. Standard formulations of such problems model a solution …
reads sequenced from all of them. Standard formulations of such problems model a solution …
On the complexity of minimum path cover with subpath constraints for multi-assembly
Background Multi-assembly problems have gathered much attention in the last years, as
Next-Generation Sequencing technologies have started being applied to mixed settings …
Next-Generation Sequencing technologies have started being applied to mixed settings …
Does relaxing the infinite sites assumption give better tumor phylogenies? An ILP-based comparative approach
P Bonizzoni, S Ciccolella… - … /ACM transactions on …, 2018 - ieeexplore.ieee.org
Most of the evolutionary history reconstruction approaches are based on the infinite sites
assumption, which states that mutations appear once in the evolutionary history. The Perfect …
assumption, which states that mutations appear once in the evolutionary history. The Perfect …
Multitrans: an algorithm for path extraction through mixed integer linear programming for transcriptome assembly
Recent advances in RNA-seq technology have made identification of expressed genes
affordable, and thus boosting repaid development of transcriptomic studies. Transcriptome …
affordable, and thus boosting repaid development of transcriptomic studies. Transcriptome …
Explaining a weighted DAG with few paths for solving genome-guided multi-assembly
RNA-Seq technology offers new high-throughput ways for transcript identification and
quantification based on short reads, and has recently attracted great interest. This is …
quantification based on short reads, and has recently attracted great interest. This is …
Towards the integration, annotation and association of historical microarray experiments with RNA-seq
Background Transcriptome analysis by microarrays has produced important advances in
biomedicine. For instance in multiple myeloma (MM), microarray approaches led to the …
biomedicine. For instance in multiple myeloma (MM), microarray approaches led to the …
Transcriptome assembly and quantification from Ion Torrent RNA-Seq data
Background High throughput RNA sequencing (RNA-Seq) can generate whole
transcriptome information at the single transcript level providing a powerful tool with multiple …
transcriptome information at the single transcript level providing a powerful tool with multiple …
Efficient minimum flow decomposition via integer linear programming
Minimum flow decomposition (MFD) is an NP-hard problem asking to decompose a network
flow into a minimum set of paths (together with associated weights). Variants of it are …
flow into a minimum set of paths (together with associated weights). Variants of it are …
[图书][B] Computational methods for next generation sequencing data analysis
Introduces readers to core algorithmic techniques for next-generation sequencing (NGS)
data analysis and discusses a wide range of computational techniques and applications …
data analysis and discusses a wide range of computational techniques and applications …
Fast, flexible, and exact minimum flow decompositions via ILP
Minimum flow decomposition (MFD)—the problem of finding a minimum set of paths that
perfectly decomposes a flow—is a classical problem in Computer Science, and variants of it …
perfectly decomposes a flow—is a classical problem in Computer Science, and variants of it …